biocko Goto Github PK

teleost-repeats

Repo for "Genomic repeat landscape evolution across the teleost fish lineages" (Reinar et al. 2019)

teleost_genomes_immune

thermoalign

ThermoAlign: software for automated primer design

tilapiasexchr

Genomics analyses for Nile tilapia and blue tilapia genomes

toga

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

tolypocladium_inflatum_paper

Scripts and customized scripts used in this paper

topaza_uce

all files and commands related to the topaza UCE allele phasing project

training-material

A collection of Galaxy-related training material

triobinningscripts

Scripts to reproduce TrioBinning manuscript

tutorials

Tutorials on phylogenetic and phylogenomic inference

tutorials-1

Tutorials on evolutionary genomics

tvedora_dev_rnaseq

In this project, we investigate the evolution and dynamics of sex-biased genes and gene expression along the five developmental stages of the common frog Rana temporaria, in a population with proto-Y chromosomes.

vert_trans

Analysis of sex chromosome evolution across the phylogeny of vertebrates

virbin

virtus2

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.

vole_genome_analysis

Material for the analysis of Microtus whole genomes

wgac

Scripts used for whole genome analysis comparison (WGAC)

wgd

Python package and CLI for whole-genome duplication analyses

wheathomoeologexpression

widespread-linked-selection

Scripts for Wang et al (2020) Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.

worm-code

x-gene-expression

Reproducing "Sex-Biased Gene Expression and Evolution of the X Chromosome in Nematodes"

xci

Scripts used for Xist-mediated chromosome silencing analysis work

xvautosomeinversions

xy_rnaseq

Alignment and filtering effects on RNAseq analysis on the X and Y chromosomes

xy_rnaseq-1

xydiversity

Code used for population genetic analyses of X and Y chromosomes in Rumex hastatulus

y-amplicon-evolution

Scripts used in Teitz et. al 2018

y-chromosome

yhaplo

Identifying Y-chromosome haplogroups in arbitrarily large samples of sequenced or genotyped men